\name{pRRopheticPredict}
\alias{pRRopheticPredict}
\title{Given a gene expression matrix, predict drug senstivity for a drug in CGP}
\usage{
pRRopheticPredict(testMatrix, drug, tissueType = "all", doCV = FALSE,
  batchCorrect = "eb", powerTransformPhenotype = TRUE,
  removeLowVaryingGenes = 0.2, minNumSamples = 10, selection = -1,
  printOutput = TRUE)
}
\arguments{
  \item{testMatrix}{a gene expression matrix with gene
  names as row ids and sample names as column ids.}

  \item{drug}{the name of the drug for which you would like
  to predict sensitivity, one of A.443654, A.770041,
  ABT.263, ABT.888, AG.014699, AICAR, AKT.inhibitor.VIII,
  AMG.706, AP.24534, AS601245, ATRA, AUY922, Axitinib,
  AZ628, AZD.0530, AZD.2281, AZD6244, AZD6482, AZD7762,
  AZD8055, BAY.61.3606, Bexarotene, BI.2536, BIBW2992,
  Bicalutamide, BI.D1870, BIRB.0796, Bleomycin, BMS.509744,
  BMS.536924, BMS.708163, BMS.754807, Bortezomib,
  Bosutinib, Bryostatin.1, BX.795, Camptothecin, CCT007093,
  CCT018159, CEP.701, CGP.082996, CGP.60474, CHIR.99021,
  CI.1040, Cisplatin, CMK, Cyclopamine, Cytarabine,
  Dasatinib, DMOG, Docetaxel, Doxorubicin, EHT.1864,
  Elesclomol, Embelin, Epothilone.B, Erlotinib, Etoposide,
  FH535, FTI.277, GDC.0449, GDC0941, Gefitinib,
  Gemcitabine, GNF.2, GSK269962A, GSK.650394, GW.441756,
  GW843682X, Imatinib, IPA.3, JNJ.26854165, JNK.9L,
  JNK.Inhibitor.VIII, JW.7.52.1, KIN001.135, KU.55933,
  Lapatinib, Lenalidomide, LFM.A13, Metformin,
  Methotrexate, MG.132, Midostaurin, Mitomycin.C, MK.2206,
  MS.275, Nilotinib, NSC.87877, NU.7441, Nutlin.3a,
  NVP.BEZ235, NVP.TAE684, Obatoclax.Mesylate, OSI.906,
  PAC.1, Paclitaxel, Parthenolide, Pazopanib, PD.0325901,
  PD.0332991, PD.173074, PF.02341066, PF.4708671,
  PF.562271, PHA.665752, PLX4720, Pyrimethamine, QS11,
  Rapamycin, RDEA119, RO.3306, Roscovitine, Salubrinal,
  SB.216763, SB590885, Shikonin, SL.0101.1, Sorafenib,
  S.Trityl.L.cysteine, Sunitinib, Temsirolimus,
  Thapsigargin, Tipifarnib, TW.37, Vinblastine,
  Vinorelbine, Vorinostat, VX.680, VX.702, WH.4.023,
  WO2009093972, WZ.1.84, X17.AAG, X681640, XMD8.85,
  Z.LLNle.CHO, ZM.447439.}

  \item{tissueType}{specify if you would like to traing the
  models on only a subset of the CGP cell lines (based on
  the tissue type from which the cell lines originated).
  This be one any of "all" (for everything, default
  option), "allSolidTumors" (everything except for blood),
  "blood", "breast", "CNS", "GI tract" ,"lung", "skin",
  "upper aerodigestive"}

  \item{doCV}{}
}
\value{
a gene expression matrix that does not contain duplicate
gene ids
}
\description{
Given a gene expression matrix, predict drug senstivity for
a drug in CGP.
}
\keyword{by}
\keyword{duplicate}
\keyword{gene}
\keyword{ids}
\keyword{mean.}
\keyword{summarize}
\keyword{their}

